A directory of scripts that utilize the Paleobiology Database

Getting started
Submitting a script
List of scripts

If you are unfamiliar with using Git for version control, these are some good resources to get you started:

• Pro Git by Scott Chacon
• Think Like (a) Git
• Git cheatsheet
• LearnGitBranching - An interactive way to learn Git

Simply submit a pull request to this repo following the instructions below:

1. Click "Fork" in upper right corner of this page

2. You should now be at http://github.com/your_user_name/utilities. In the bottom right, copy the clone URL URL, and on your local machine open Terminal and type this, substituting your username for the placeholder: git clone https://github.com/your_user_name/analysis_tools.git

3. You now have a copy of this repository on your local machine. You can now open this file (README.md) and add your script. When you are done, save your changes.

4. Making sure you are in the correct directory, add, commit, and push your changes:

   git add -u
   git commit -m "Added my script to the list"
   git push
   

5. Go to https://github.com/your_user_name/analysis_tools/pulls and click "New pull request", and then "Create Pull Request". Write a note explaining the changes you made and click "Send pull request"! Once we get a chance to review your changes, they will show up on the list.

If you would like to add your script to this list, please refer to submitting a script above. As more scripts are added, it may become necessary to organize by language or purpose.

# Simple example to identify possibly problematic homonym genera (or duplicates
# or multiple listings of a genus, as occurs when there are subgenera) (written 
# by Phil Novack-Gottshall <[email protected]> 
pbdb <- read.csv("www.paleobiodb.org/data1.2/taxa/list.csv?base_name=Metazoa&show=app&vocab=pbdb")
# Big download! If errors, copy the URL directly into browser and save csv to working directory
which.gsg <- 
  which((pbdb$accepted_rank == "genus" | pbdb$accepted_rank == "subgenus") 
        & pbdb$difference == "")
sort(table(pbdb$accepted_name[which.gsg]), decreasing = TRUE)[1:20]
# Example (as of 9/1/2019, includes a homonym and likely duplicate entry):
pbdb[which(pbdb$accepted_name == "Lowenstamia"), ]

=========

Description: R interface to the Paleobiology Database API
Language: R
Authors: Sara Varela, Javier Gonzalez-Hernandez and Luciano Fabris Sgarbi
Project website: http://ropensci.org
Code: https://github.com/ropensci/paleobioDB

Description: Various R scripts that utilize the Paleobiology Database, including one to calculate the maximum great circle distance between any two occurrences of a taxon in a time interval
Language: R
Author: Matthew Clapham
Code: https://github.com/mclapham/PBDB-R-scripts

Description: Various R scripts that utilize the Paleobiology Database, including one to create a compact taxonomic structure and to check for homonyms or problematic duplicate genera
Language: R
Author: Phil Novack-Gottshall
Code: https://github.com/pnovack-gottshall/PBDB-R-scripts